Since ~2000, the productivity of cacao (Theobroma cacao L.) has declined in part due to cacao swollen shoot disease (CSSD), which is attributed to infection by a group of badnavirus species. To better-understand CSSD-badnavirus species diversity and genomic variability, symptomatic cacao leaf samples were collected in Cote d´Ivoire and Ghana, and the total DNA was subjected to high-throughput sequencing. The RT-RNaseH and complete genome sequences were evaluated with respect to phylogenetic informativeness and species demarcation. Nucleotide diversity and potential for recombination were determined for the badnaviral genomes. Three badnaviruses were identified among the 30 new genomes, Cacao swollen shoot virus (CSSV), Cacao swollen shoot CD virus (CSSCDV), and Cacao red vein virus (CRVV). The RDP4 analysis revealed eight independent recombination events involving West African (WA) isolates. This result was supported by the network analysis (SplitsTree4), which also evidenced recombination affecting the diversification of WA badnaviruses. High values of nucleotide diversity (?) were observed for CSSV (?=0.06691) and CSSCDV (?=0.07111), with CRVV (?=0.21911) being the most variable among the three species. Purifying selection was the main selective force identified among the CSSV isolates. Phylogenetic trees reconstructed for the viral ORFs 1-2, RT-RNaseH, and MP, separately, were incongruent with one another and with the complete CSSD-badnaviral genome tree.